A speed-fidelity trade-off determines the mutation rate and virulence of an RNA virus

William Fitzsimmons; Robert J. Woods; John T. McCrone; Andrew Woodman; Jamie J. Arnold; Madhumita Yennawar; Richard Evans; Craig E. Cameron; Adam S. Lauring

We next compared the phenotype of WT and 3D G64S viruses in vivo, where the ability to 198 generate genetic diversity may allow a virus to escape host immune restriction and to replicate 199 better in a range of environments. Importantly, the available data have suggested that the 200 attenuation of 3D G64S and other high fidelity variants in experimental models is attributable to 201 differences in the genetic diversity of the infecting population [7] . We therefore used next 202 generation sequencing to compare the genetic diversity of 5 replicate stocks each of WT and 203 3D G64S . Using an internally benchmarked analysis pipeline that dramatically reduces false 204 positive variant calls (see [46] and Methods), we identified no variants at greater than 0.1% 205 frequency. Therefore, we can exclude any significant differences in standing genetic diversity 206 between our WT and 3D G64S populations. Even at extremely high multiplicities of infection, 9 variants present at <0.1% are unlikely to complement each other or to cooperate reproducibly in 208 a cellular context or in vivo [47] .